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<a href="#namespaces">Namespaces</a> &#124;
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<p>The moltk namespace contains everything in the MolTK C++ API.  
<a href="#details">More...</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="namespaces"></a>
Namespaces</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk_1_1units.html">units</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><p>The <a class="el" href="namespacemoltk_1_1units.html" title="The moltk::units namespace contains physical Quantities, Units, and Dimensions.">moltk::units</a> namespace contains physical Quantities, Units, and Dimensions. </p>
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Classes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html">Aligner</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">The <a class="el" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a> class creates macromolecule sequence alignments and structure alignments.  <a href="classmoltk_1_1Aligner.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> represents a set of aligned macromolecule sequences and/or structures.  <a href="classmoltk_1_1Alignment.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1BaseBiosequence.html">BaseBiosequence</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Parent class for macromolecule sequences and structures.  <a href="classmoltk_1_1BaseBiosequence.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1BiosequenceResidue.html">BiosequenceResidue</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">One residue in a macromolecule sequence (a nucleotide or amino acid)  <a href="classmoltk_1_1BiosequenceResidue.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">A macromolecule sequence (DNA or RNA or protein)  <a href="classmoltk_1_1Biosequence.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html">EString</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">A compact representation of the gapping pattern for one sequence in an alignment.  <a href="classmoltk_1_1EString.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html">MatrixScorer</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1MatrixScorer.html" title="MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250.">MatrixScorer</a> scores alignments using a residue type matrix such as BLOSUM62 or PAM250.  <a href="classmoltk_1_1MatrixScorer.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1PDBStructure.html">PDBStructure</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1PDBStructure.html" title="PDBStructure represents a macromolecule structure as found in a Protein Data Bank file...">PDBStructure</a> represents a macromolecule structure as found in a Protein Data Bank file.  <a href="classmoltk_1_1PDBStructure.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Printable.html">Printable</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Printable.html" title="moltk::Printable is an abstract base class to help streamline string conversion in the moltk python b...">moltk::Printable</a> is an abstract base class to help streamline string conversion in the moltk python bindings.  <a href="classmoltk_1_1Printable.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Quaternion.html">Quaternion</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Quaternion.html" title="Quaternion is an elegant 4-element representation of a 3D rotation.">Quaternion</a> is an elegant 4-element representation of a 3D rotation.  <a href="classmoltk_1_1Quaternion.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1RigidTransform.html">RigidTransform</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1RigidTransform.html" title="RigidTransform converts one reference frame to another with rotation and translation.">RigidTransform</a> converts one reference frame to another with rotation and translation.  <a href="classmoltk_1_1RigidTransform.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Rotation3D.html">Rotation3D</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Rotation3D.html" title="Rotation3D represents a rotation matrix.">Rotation3D</a> represents a rotation matrix.  <a href="classmoltk_1_1Rotation3D.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1BaseVector3D.html">BaseVector3D</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1BaseVector3D.html" title="BaseVector3D is a parent class for points and vectors.">BaseVector3D</a> is a parent class for points and vectors.  <a href="classmoltk_1_1BaseVector3D.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Vector3D__.html">Vector3D_</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Vector3D_&lt;&gt; is an arbitrary point or vector in 3-space.  <a href="classmoltk_1_1Vector3D__.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1UnitVector3D.html">UnitVector3D</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1UnitVector3D.html" title="UnitVector3D represents a direction in 3 space, and, unlike Vector3D_&lt;&gt;, does NOT have Units...">UnitVector3D</a> represents a direction in 3 space, and, unlike Vector3D_&lt;&gt;, does NOT have Units.  <a href="classmoltk_1_1UnitVector3D.html#details">More...</a><br/></td></tr>
<tr><td colspan="2"><h2><a name="typedef-members"></a>
Typedefs</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk.html#afe6fbd8f5686b34143c2742fcc97292c">Real</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Real represents a real number, such as 5.6.  <a href="#afe6fbd8f5686b34143c2742fcc97292c"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classmoltk_1_1Vector3D__.html">Vector3D_</a>&lt; <a class="el" href="namespacemoltk.html#afe6fbd8f5686b34143c2742fcc97292c">moltk::Real</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk.html#a57c8d4c46298003a12cee6972290fca0">Vector3D</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Vector3D is an arbitrary unitless vector or point in 3 space.  <a href="#a57c8d4c46298003a12cee6972290fca0"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classmoltk_1_1Vector3D__.html">Vector3D_</a><br class="typebreak"/>
&lt; <a class="el" href="namespacemoltk_1_1units.html#a5800c5371d9ddac68ae3edf51b0e3881">moltk::units::Length</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk.html#a13b47fe109e93238de3d383f378db960">Displacement</a></td></tr>
<tr><td colspan="2"><h2><a name="func-members"></a>
Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk.html#a403bc85428d8dd3e1b17e60f2968dc1d">align</a> (const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;target_alignment, const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;query_alignment)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk.html#a5d6a32006fb76447d32cde962b6ab1fb">load_fasta</a> (const std::string &amp;file_name)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">global load_fasta method helps get SEQUOIA-like conciseness in python.  <a href="#a5d6a32006fb76447d32cde962b6ab1fb"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::istream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk.html#a9d6101e75a7b6c533c256d3bceeae415">operator&gt;&gt;</a> (std::istream &amp;, <a class="el" href="classmoltk_1_1MatrixScorer.html">moltk::MatrixScorer</a> &amp;)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::ostream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk.html#aef749887c79b7809fd7f8d0b14dd1285">operator&lt;&lt;</a> (std::ostream &amp;output_stream, const <a class="el" href="classmoltk_1_1Printable.html">moltk::Printable</a> &amp;printable)</td></tr>
<tr><td class="memTemplParams" colspan="2">template&lt;class D , class Y &gt; </td></tr>
<tr><td class="memTemplItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Vector3D__.html">Vector3D_</a><br class="typebreak"/>
&lt; <a class="el" href="structmoltk_1_1units_1_1Quantity.html">moltk::units::Quantity</a><br class="typebreak"/>
&lt; <a class="el" href="structmoltk_1_1units_1_1Unit.html">moltk::units::Unit</a>&lt; D &gt;, Y &gt; &gt;&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="namespacemoltk.html#aa16426817d5a9f5001105331496d3022">operator*</a> (const <a class="el" href="classmoltk_1_1Vector3D__.html">Vector3D_</a>&lt; Y &gt; &amp;vector, const <a class="el" href="structmoltk_1_1units_1_1Unit.html">moltk::units::Unit</a>&lt; D &gt; &amp;unit)</td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>The moltk namespace contains everything in the MolTK C++ API. </p>
</div><hr/><h2>Typedef Documentation</h2>
<a class="anchor" id="a13b47fe109e93238de3d383f378db960"></a><!-- doxytag: member="moltk::Displacement" ref="a13b47fe109e93238de3d383f378db960" args="" -->
<div class="memitem">
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      <table class="memname">
        <tr>
          <td class="memname">typedef <a class="el" href="classmoltk_1_1Vector3D__.html">Vector3D_</a>&lt; <a class="el" href="namespacemoltk_1_1units.html#a5800c5371d9ddac68ae3edf51b0e3881">moltk::units::Length</a> &gt; <a class="el" href="namespacemoltk.html#a13b47fe109e93238de3d383f378db960">moltk::Displacement</a></td>
        </tr>
      </table>
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<div class="memdoc">

</div>
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<a class="anchor" id="afe6fbd8f5686b34143c2742fcc97292c"></a><!-- doxytag: member="moltk::Real" ref="afe6fbd8f5686b34143c2742fcc97292c" args="" -->
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      <table class="memname">
        <tr>
          <td class="memname">typedef double <a class="el" href="namespacemoltk.html#afe6fbd8f5686b34143c2742fcc97292c">moltk::Real</a></td>
        </tr>
      </table>
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<div class="memdoc">

<p>Real represents a real number, such as 5.6. </p>

</div>
</div>
<a class="anchor" id="a57c8d4c46298003a12cee6972290fca0"></a><!-- doxytag: member="moltk::Vector3D" ref="a57c8d4c46298003a12cee6972290fca0" args="" -->
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          <td class="memname">typedef <a class="el" href="classmoltk_1_1Vector3D__.html">Vector3D_</a>&lt; <a class="el" href="namespacemoltk.html#afe6fbd8f5686b34143c2742fcc97292c">moltk::Real</a> &gt; <a class="el" href="namespacemoltk.html#a57c8d4c46298003a12cee6972290fca0">moltk::Vector3D</a></td>
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<p>Vector3D is an arbitrary unitless vector or point in 3 space. </p>

</div>
</div>
<hr/><h2>Function Documentation</h2>
<a class="anchor" id="a403bc85428d8dd3e1b17e60f2968dc1d"></a><!-- doxytag: member="moltk::align" ref="a403bc85428d8dd3e1b17e60f2968dc1d" args="(const Alignment &amp;target_alignment, const Alignment &amp;query_alignment)" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> moltk::align </td>
          <td>(</td>
          <td class="paramtype">const Alignment &amp;&#160;</td>
          <td class="paramname"><em>target_alignment</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const Alignment &amp;&#160;</td>
          <td class="paramname"><em>query_alignment</em>&#160;</td>
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          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
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<a class="anchor" id="a5d6a32006fb76447d32cde962b6ab1fb"></a><!-- doxytag: member="moltk::load_fasta" ref="a5d6a32006fb76447d32cde962b6ab1fb" args="(const std::string &amp;file_name)" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> moltk::load_fasta </td>
          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>file_name</em></td><td>)</td>
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<p>global load_fasta method helps get SEQUOIA-like conciseness in python. </p>

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<a class="anchor" id="aa16426817d5a9f5001105331496d3022"></a><!-- doxytag: member="moltk::operator*" ref="aa16426817d5a9f5001105331496d3022" args="(const Vector3D_&lt; Y &gt; &amp;vector, const moltk::units::Unit&lt; D &gt; &amp;unit)" -->
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template&lt;class D , class Y &gt; </div>
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          <td class="memname"><a class="el" href="classmoltk_1_1Vector3D__.html">Vector3D_</a>&lt;<a class="el" href="structmoltk_1_1units_1_1Quantity.html">moltk::units::Quantity</a>&lt;<a class="el" href="structmoltk_1_1units_1_1Unit.html">moltk::units::Unit</a>&lt;D&gt;, Y&gt; &gt; moltk::operator* </td>
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          <td class="paramtype">const Vector3D_&lt; Y &gt; &amp;&#160;</td>
          <td class="paramname"><em>vector</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="structmoltk_1_1units_1_1Unit.html">moltk::units::Unit</a>&lt; D &gt; &amp;&#160;</td>
          <td class="paramname"><em>unit</em>&#160;</td>
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          <td></td>
          <td>)</td>
          <td></td><td></td>
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<a class="anchor" id="aef749887c79b7809fd7f8d0b14dd1285"></a><!-- doxytag: member="moltk::operator&lt;&lt;" ref="aef749887c79b7809fd7f8d0b14dd1285" args="(std::ostream &amp;output_stream, const moltk::Printable &amp;printable)" -->
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          <td class="memname">std::ostream&amp; moltk::operator&lt;&lt; </td>
          <td>(</td>
          <td class="paramtype">std::ostream &amp;&#160;</td>
          <td class="paramname"><em>output_stream</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Printable.html">moltk::Printable</a> &amp;&#160;</td>
          <td class="paramname"><em>printable</em>&#160;</td>
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          <td></td>
          <td>)</td>
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